Genome assembly and comparative analysis of Alternaria linariae reveal novel genes associated with host colonization and virulence
Abstract Background Early blight (EB) is one of the most economically devastating diseases affecting tomato production, leading to significant yield losses. Traditionally, EB has been associated with the fungus Alternaria solani. However, recent evidence indicates that A. linariae (previously known...
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| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2025-07-01
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| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12864-025-11819-z |
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| Summary: | Abstract Background Early blight (EB) is one of the most economically devastating diseases affecting tomato production, leading to significant yield losses. Traditionally, EB has been associated with the fungus Alternaria solani. However, recent evidence indicates that A. linariae (previously known as A. tomatophila) is the main causative agent. This revised understanding improves diagnostic accuracy and underscores A. linariae as a valuable resource for studying host-pathogen interactions, host adaptation, and evolutionary mechanisms within the Alternaria genus due to its distinct pathogenic profile and host specificity. Methodology The A. linariae strain 25, isolated from EB-infected tomatoes in Swain County, North Carolina, United States, was confirmed through analyses of its asexual morphs, cultural characteristics, and PCR-based identification. Nonetheless, the genomic structure and genetic factors influencing host specificity in A. linariae on tomatoes remain poorly understood. To address this knowledge gap, we sequenced the complete genome of A. linariae. This study will help elucidate its structure, compare its genomic features with those of other Alternaria spp., and identify the genetic basis for its host specificity. These insights are crucial for understanding its pathogenicity and host adaptation and for developing effective disease management strategies. Results The genome of A. linariae strain 25 has been fully assembled and spans 33.1 Mb. It comprises 18 rRNA genes and 117 tRNA genes, and approximately 272,542 base pairs (0.8%) of repetitive elements. The genome features 11,768 predicted gene models, with 221 genes identified as potential candidate effector proteins that may play a role in host colonization and specificity. Additionally, the genome encodes 573 carbohydrate-active enzymes (CAZymes) and 37 secondary metabolite gene clusters, which are likely involved in pathogenicity and interactions with the host. Conclusion A comparative genomic analysis of effector genes across different Alternaria spp. revealed that the A. linariae strain 25 possesses unique effectors, which may enhance its ability to colonize and adapt precisely to tomato plants. These findings lay the groundwork for further investigation into the molecular mechanisms that drive host specificity and pathogenicity in A. linariae and provide a foundation for developing targeted strategies to control early blight in tomato crops. |
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| ISSN: | 1471-2164 |